Add astrocyte_lr_1994 to NEST for the modeling of astrocytes and neuron-astrocyte interactions#2919
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heplesser merged 195 commits intonest:masterfrom Sep 15, 2023
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… NEST version. Also add a python example of using the astrocyte component
…oulliAstroBuilder
… when p_astro is not given; assigning or overlapping not possible yet
…astrocytes connecting to neurons without presynaptic sources
… paired with astrocyte" instead of "target neurons paired with astrocyte"; "weight_astro" in syn_spec renamed as "weight_sic"
- True/False for Deterministic/Probabilistic selection of astrocyte pool per target neuron. - Rename "p_astro" to "p_syn_astro" since this parameter defines the probability of a neuron-neuron synapse being paired with an astrocyte.
- Set default to true - When true, the default of "max_astro_per_target" is 1 - When false, the default of "max_astro_per_target" is 0 (all astrocytes can connect)
…_per_target_det and (B) max_astro_per_target. - A=True, B=None: Distribute the neurons according to N_neuron/N_astrocyte. - A=True, B=n: Make overlapping in uneven cases more balanced (still to be improved). - Debug: p=1 is OK now, but autapses must be allowed. To be discussed.
…mber of max_astro_per_target.
…ivity - Fix the special case of: autapses not allowed, p=1, target overlaps with sources
HanjiaJiang
commented
Sep 14, 2023
…ator into hanjia_lr_1994
Pull request to fix test problem
pnbabu
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Sep 15, 2023
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The changes look good to me. Thanks!
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@HanjiaJiang Thank you very much for your efforts in polishing the PR. It is fine now and we can merge as soon as the tests have completed successfully.
terhorstd
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astrocyte_lr_1994 to NEST for the modeling of astrocytes and neuron-astrocyte interactions
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We implemented an astrocyte model (astrocyte_lr_1994) based on the paper by Li & Rinzel (1994), for the study of astrocytes and neuron-astrocyte interactions in NEST. A new connection type (sic_connection) and a new neuron type (aeif_cond_alpha_astro) were also implemented for this purpose. We also created two example scripts for astrocyte dynamics, two test files for astrocyte_lr_1994 and sic_connection respectively, and one jupyter notebook file as a reference of model implementation.
The code is co-authored by Jugoslava Aćimović, Jan Hahne, Han-Jia Jiang, Mikko Lehtimäki, Tiina Manninen, and Jonas Stapmanns.